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Elusive does not always equal rare: Genetic assessment of a protected Gila monster (Heloderma suspectum) population in Saguaro National Park, Arizona
Abstract
Population genetic baselines for species perceived to be at-risk are crucial for monitoring population trends and making well-informed management decisions. We characterized the genetic status of a population of Gila monsters (Heloderma suspectum), a large venomous lizard native to deserts of the southwestern United States and northern Mexico, by sampling 100 individuals in Sonoran Desert upland habitat at Saguaro National Park, Arizona, USA. We used 18 microsatellite markers, along with 1195 bp of sequence data from the mitochondrial DNA 12S locus, to examine genetic diversity, estimate effective population size, and assess demographic history. Despite suburban development adjacent to the study area, we observed high genetic diversity with uninhibited gene flow within this protected population. We estimated effective population size (Ne) for the total sample area (80 km2) using the linkage disequilibrium method in NeEstimator to be 94 individuals (95% confidence interval: 80.7-111.2). In 2011, we used capture-recapture methods to estimate that 80 adult Gila monsters (95% CI = 37-225) inhabited the area along the 14-km transect that we surveyed most frequently; probability of detecting resident Gila monsters during surveys was <0.01, highlighting the challenges of studying the species. Despite being considered an elusive and thus potentially rare species, these data reveal that in this protected environment the population appears healthy and robust. The results provide an important genetic baseline for future studies and monitoring, and exemplify the success of protective population measures in National Parks and under Arizona state laws.
... Nevertheless, RC is often regarded as a valuable method to locate H. suspectum. For example, Farrar et al. (2017) found most of their 100 individuals from roads rather than on foot. ...
Numerous references suggest road cruising is effective for detecting many lizard taxa, yet standard inventory and monitoring publications invariably emphasize the technique to target snakes, turtles, and amphibians, with little to no mention of its use for lizards. Instead, the most commonly employed methods to detect surface-active lizard species are various visual surveys on foot. At two study sites in Arizona, USA, we used very low-speed, diurnal road cruising to detect surface-active lizards from a vehicle. To determine the efficacy of the method compared to a more conventional one, we compared our results to those of adjacent walking surveys. Between the two studies and two methods, we detected 16 lizard species. Both approaches were generally effective at targeting the same heliothermic species, although there were some differences in encounter rates. Individuals of all species were more likely to flee from an observer on foot than one in a car. Because of this differential flight response, the proportion of unidentifiable species was significantly higher from foot searches than from a vehicle.
... Popular insects (e.g., the Monarch butterfly and the American giant stag beetle; Zhan et al. 2014;Pfeiler et al. 2017;Ulyshen et al. 2017) have been foci of conservation, and successful conservation plans for the European stag beetle have promoted both the preservation of regional biodiversity and public awareness of protecting and creating habitats for local biota (Harvey and Gange 2011). In addition to endemic vertebrates (see, e.g., Farrar et al. 2017), the Western Hercules beetle can serve as an insect flagship species for conserving the biodiversity of the unique highland forest habitats of southwestern United States. The large body size, unique body coloration and pattern, and exaggerated structure of the adult male horn ( Figure 1B) make these beetles popular pets and trophies for private collections (McMonigle 2012). ...
The Western Hercules beetle (Dynastes grantii) is endemic to the highland forest habitats of southwestern USA and northern Mexico. The habitats harbor many endemic species, but are being threatened by rapid climate change and urban development. In this study, the genetic structure of D. grantii populations from southwestern USA was investigated. Specifically, genomic data from double-digest RADseq (ddRADseq) libraries were utilized to test whether geographically distant populations from the Mogollon Rim (Arizona [N = 12 individuals] and New Mexico [N = 10 individuals]) are genetically structured. The study also estimated the effective population size of the Mogollon Rim populations based on genetic diversity. The results indicated that the two geographic populations from the Mogollon Rim were not genetically structured. A population size reduction was detected since the end of the last glacial period, which coincided with a reduction of forest habitat in the study area. The results implied that the connectivity and the size of highland forest habitats in the Mogollon Rim could have been the major factors shaping the population genetic structure and demographic history of D. grantii. The Western Hercules beetle could be a useful flagship species for local natural history education and to promote the conservation of highland forest habitats.
Arlequin ver 3.0 is a software package integrating several basic and advanced methods for population genetics data analysis, like the computation of standard genetic diversity indices, the estimation of allele and haplotype frequencies, tests of departure from linkage equilibrium, departure from selective neutrality and demographic equilibrium, estimation or parameters from past population expansions, and thorough analyses of population subdivision under the AMOVA framework. Arlequin 3 introduces a completely new graphical interface written in C++, a more robust semantic analysis of input files, and two new methods: a Bayesian estimation of gametic phase from multi-locus genotypes, and an estimation of the parameters of an instantaneous spatial expansion from DNA sequence polymorphism. Arlequin can handle several data types like DNA sequences, microsatellite data, or standard multilocus genotypes. A Windows version of the software is freely available on http://cmpg.unibe.ch/software/arlequin3.
Assessment of population structure is critical to the design and implementation of sound management and conservation strategies. However, population structure must be assessed using markers attuned to population genetic processes such as genetic drift and gene flow, which reflect actual levels of reproductive isolation among putative genetic clusters. This is critical for highly exploited, commercial species that form the backbone of regional and local economies. Here, we show extremely low levels of population genetic differentiation among Greenland halibut (Reinhardtius hippoglossoides) collected from throughout the Northwest Atlantic, which cannot be statistically differentiated from panmixia using 12 species-specific polymorphic microsatellite markers. In contrast, some previous studies have demonstrated significant differences among individuals collected from various parts of the species’ range using a variety of both genetic and nongenetic techniques. In accordance with other reports and consistent with the species’ life history, we demonstrate that the most parsimonious explanation reconciling observed patterns is a repeated high degree of local differentiation of new recruits and colonizers originating from a common gene pool. Such a scenario has important conservation implications in terms of devising more appropriate strategies balancing species persistence and replenishment with sustainable resource use.
Buffel grass [Pennisetum ciliare (L.) Link] has been widely introduced in the Australian rangelands as a consequence of its value for productive grazing, but tends to competitively establish in non-target areas such as remnant vegetation. In this study, we examined the influence landscape-scale and local-scale variables had upon the distribution of buffel grass in remnant poplar box (Eucalyptus populnea F. Muell.) dominant woodland fragments in the Brigalow Bioregion, Queensland. Buffel grass and variables thought to influence its distribution in the region were measured at 60 sites, which were selected based on the amount of native woodland retained in the landscape and patch size. An information-theoretic modelling approach and hierarchical partitioning revealed that the most influential variable was the percent of retained vegetation within a 1-km spatial extent. From this, we identified a critical threshold of similar to 30% retained vegetation in the landscape, above which the model predicted buffel grass was not likely to occur in a woodland fragment. Other explanatory variables in the model were site based, and included litter cover and long-term rainfall. Given the paucity of information on the effect of buffel grass upon biodiversity values, we undertook exploratory analyses to determine whether buffel grass cover influenced the distribution of grass, forb and reptile species. We detected some trends; hierarchical partitioning revealed that buffel grass cover was the most important explanatory variable describing habitat preferences of four reptile species. However, establishing causal links - particularly between native grass and forb species and buffel grass - was problematic owing to possible confounding with grazing pressure. We conclude with a set of management recommendations aimed at reducing the spread of buffel grass into remnant woodlands.
Pupfishes (genus Cyprinodon) are iconic of biodiversity and endemism in the desert southwest of North America. Most of these species are imperiled, primarily because of excessive exploitation of water resources in this arid region. The critically endangered Julimes pupfish, Cyprinodon julimes, is restricted to a small, isolated, and highly modified desert spring in Chihuahua, México. We evaluated effective population size (microsatellites) and genetic variation (microsatellites and mitochondrial DNA) to determine the conservation genetic status of this species. The effective population size was critically low and indicated that this pupfish is at genetic risk of extinction through loss of adaptive variance and, potentially, from inbreeding depression. Mitochondrial variation was also extremely low, and haplotype frequency was biased heavily in favor of one of two variants. The uncommon haplotype was derived from a past hybridization event with the closely related C. eximius; whether cessation of introgressive hybridization is relevant to conservation management of Julimes pupfish is unknown but may be important to consider. Minimally, C. julimes is compromised genetically. Baseline population genetic information provided by this study will be vital to long-term monitoring of this highly imperiled species.
The number of newly discovered Malagasy vertebrate taxa has multiplied in recent years, emphasizing the importance of complete taxon sampling for phylogenetics, biogeography, functional ecology, and conservation biology, especially in such a biodiversity hotspot. In particular, the diversity of extant lemurs is much higher than previously thought, and we have yet to comprehend fully the full extent of lemuriform biodiversity. A recent genetic analysis of mtDNA and nDNA sequence data in Malagasy mouse lemurs revealed the existence of several novel mtDNA clades based on new field sampling. These geographically defined and previously unrecognized mtDNA clades corresponded precisely to patterns of population structure revealed in the analysis of the nDNA data, thus confirming their evolutionary divergence from other mouse lemur clades. Two of these independently evolving lineages correspond to specimens that were collected by us in the Marolambo and Manantantely/Ivorona regions. Here we summarize the genetic evidence and report on the morphometric and external characteristics of these animals, formally describing them as new species. This report thus brings the number of currently recognized and described mouse lemur species to 20. The forests in which these mouse lemurs were discovered have been heavily degraded in the past decade, prompting the classification of one of the new species as Endangered by the IUCN, even before its formal description. As with several other newly described lemur species, immediate field studies and appropriate conservation actions are therefore urgent.
We present the first comprehensive taxonomic revision and review the biology of the olingos, the endemic Neotropical procyonid genus Bassaricyon, based on most specimens available in museums, and with data derived from anatomy, morphometrics, mitochondrial and nuclear DNA, field observations, and geographic range modeling. Species of Bassaricyon are primarily forest-living, arboreal, nocturnal, frugivorous, and solitary, and have one young at a time. We demonstrate that four olingo species can be recognized, including a Central American species (Bassaricyon gabbii), lowland species with eastern, cis-Andean (Bassaricyon alleni) and western, trans-Andean (Bassaricyon medius) distributions, and a species endemic to cloud forests in the Andes. The oldest evolutionary divergence in the genus is between this last species, endemic to the Andes of Colombia and Ecuador, and all other species, which occur in lower elevation habitats. Surprisingly, this Andean endemic species, which we call the Olinguito, has never been previously described; it represents a new species in the order Carnivora and is the smallest living member of the family Procyonidae. We report on the biology of this new species based on information from museum specimens, niche modeling, and fieldwork in western Ecuador, and describe four Olinguito subspecies based on morphological distinctions across different regions of the Northern Andes.
NeEstimator v2 is a completely revised and updated implementation of software that produces estimates of contemporary effective population size, using several different methods and a single input file. NeEstimator v2 includes three single-sample estimators (updated versions of the linkage disequilibrium and heterozygote-excess methods, and a new method based on molecular coancestry), as well as the two-sample (moment-based temporal) method. New features include the following: (i) an improved method for accounting for missing data; (ii) options for screening out rare alleles; (iii) confidence intervals for all methods; (iv) the ability to analyse data sets with large numbers of genetic markers (10 000 or more); (v) options for batch processing large numbers of different data sets, which will facilitate cross-method comparisons using simulated data; and (vi) correction for temporal estimates when individuals sampled are not removed from the population (Plan I sampling). The user is given considerable control over input data and composition, and format of output files. The freely available software has a new JAVA interface and runs under MacOS, Linux and Windows.
Genetic diversity was examined in pronghorn (Antilocapra americana) to assess relationships among Arizona populations sharing common reintroduction or translocation sources. Ninety-seven Arizona pronghorn were analyzed for mitochondrial DNA (mtDNA) haplotype variation via restriction enzyme analysis and four composite haplotypes were revealed. Comparative analyses of Arizona pronghorn populations that shared founders from Montana, Wyoming, Texas, or central Arizona were performed. In addition, analyses of differences in haplotype frequency were performed specifically for populations in the northwestern and southeastern sections of the state because these populations are thought to be composed entirely of reint roduced pronghorn. Tests for differences in haplotype frequencies among populations sharing founders were performed using Monte Carlo simulation. Populations which received translocated animals from Texas, Wyoming, or Montana showed no significant variability in haplotype frequencies. Haplotype frequencies were significantly different among populations that received reintroductions from central Arizona only when a population which also received pronghorn from Montana, was included in analyses. Overall, populations in southeastern Arizona differed significantly from each other in haplotype frequencies. However, populations within southeastern Arizona with common reintroduction sources (e.g., Texas or central Arizona only) were not different in haplotype frequencies. Populations sampled in northwestern Arizona were not different from each other in haplotype frequencies despite the wide array of sources (central Arizona, Montana, Wyoming, Colorado, and Utah) used to restock that region. Our results suggest that whenever possible, genetic data should be used to plan future reintroductions of pronghorn in Arizona. PROCEEDINGS PRONGHORN ANTELOPE WORKSHOP 19:45-54
Traditional methods for characterizing genetic differentiation among populations rely on a priori grouping of individuals. Bayesian clustering methods avoid this limitation by using linkage and Hardy–Weinberg disequilibrium to decompose a sample of individuals into genetically distinct groups. There are several software programs available for Bayesian clustering analyses, all of which describe a decrease in the ability to detect distinct clusters as levels of genetic differentiation among populations decrease. However, no study has yet compared the performance of such methods at low levels of population differentiation, which may be common in species where populations have experienced recent separation or high levels of gene flow. We used simulated data to evaluate the performance of three Bayesian clustering software programs, PARTITION, STRUCTURE, and BAPS, at levels of population differentiation below F
ST=0.1. PARTITION was unable to correctly identify the number of subpopulations until levels of F
ST reached around 0.09. Both STRUCTURE and BAPS performed very well at low levels of population differentiation, and were able to correctly identify the number of subpopulations at F
ST around 0.03. The average proportion of an individual’s genome assigned to its true population of origin increased with increasing F
ST for both programs, reaching over 92% at an F
ST of 0.05. The average number of misassignments (assignments to the incorrect subpopulation) continued to decrease as F
ST increased, and when F
ST was 0.05, fewer than 3% of individuals were misassigned using either program. Both STRUCTURE and BAPS worked extremely well for inferring the number of clusters when clusters were not well-differentiated (F
ST=0.02–0.03), but our results suggest that F
ST must be at least 0.05 to reach an assignment accuracy of greater than 97%.
AFLP markers are often used to study patterns of population genetic variation and gene flow because they offer a good coverage of the nuclear genome, but the reliability of AFLP scoring is critical. To assess interspecific gene flow in two African rainforest liana species (Haumania danckelmaniana, H. liebrechtsiana) where previous evidence of chloroplast captures questioned the importance of hybridization and species boundaries, we developed new AFLP markers and a novel approach to select reliable bands from their degree of reproducibility. The latter is based on the estimation of the broad-sense heritability of AFLP phenotypes, an improvement over classical scoring error rates, which showed that the polymorphism of most AFLP bands was affected by a substantial nongenetic component. Therefore, using a quantitative genetics framework, we also modified an existing estimator of pairwise kinship coefficient between individuals correcting for the limited heritability of markers. Bayesian clustering confirms the recognition of the two Haumania species. Nevertheless, the decay of the relatedness between individuals of distinct species with geographic distance demonstrates that hybridization affects the nuclear genome. In conclusion, although we showed that AFLP markers might be substantially affected by nongenetic factors, their analysis using the new methods developed considerably advanced our understanding of the pattern of gene flow in our model species.
Estimamos la riqueza de especies, su distribución y la abundancia relativa de herpetofauna a lo largo de un gradiente de 1,800 m de elevación en las montañas Rincon durante 2001 y 2002 y comparamos los patrones de la presencia de especies en otras sierras en el sureste de Arizona. Detectamos 2,378 individuos de 40 especies durante 596 horas de muestreos visuales, y 1,793 más individuos colectados incidentalmente (incluyendo otras seis especies). Con base en métodos de probabilidad, estimamos que ≤57 especies probablemente ocurren en las montañas Rincon; observaciones anteriores también sugieren que ≤57 especies probablemente se encuentran allá. La riqueza de especies disminuyó con el incremento en la elevación; la abundancia relativa disminuyó con el aumento en la elevación para siete especies, aumentó con la elevación para tres especies y fue mayor en elevaciones medias para tres especies. Las montañas Rincon carecen de algunas especies que ocurren en cordilleras cercanas de tamaño y elevación similar, debido posiblemente a factores climáticos o históricos. Nuestro estudio fue el primer inventario detallado de herpetofauna en las montañas Rincon al mismo tiempo que estas comunidades pueden estar sufriendo cambios importantes.
Cell cultures have been established from 33 individual black rhinoceroses. These were from wild populations from various localities in southern Africa and include representatives from three geographical regions (southwestern, south-central, and eastern) corresponding to currently accepted conservation units, and include individuals previously attributed to one of the four subspecies, Diceros b. minor, D. b. bicornis, D. b. michaeli, and D. b. chobiensis (du Toit et al. 1987). Comparative mitochondrial DNA restriction maps were constructed using 16 restriction enzymes. These showed in each case two site differences between representative individuals from any two of the above geographical regions. Maps were monomorphic within geographical regions and, therefore, have the potential to provide diagnostic markers. The map from a single individual attributed to the D. b. chobiensis subspecies was identical to other individuals (attributed to D. b. minor) in the south-central geographical region. The low amount of genetic diversity implied by these few differences renders it unlikely that problems with outbreeding depression will arise if, given the continuing decline in numbers of black rhinoceroses, it becomes necessary to supplement wild or captive populations with individuals from a different conservation unit in order to avoid inbreeding depression.
To assess whether urbanization influences the spatial ecology of a rare and protected venomous reptilian predator, the Gila monster Heloderma suspectum, we compared home range (HR) size and movement parameters at three sites varying in degree of urbanization in the Sonoran Desert. We predicted that the urban population of H. suspectum would exhibit smaller HRs, avoid human structures and show less movement. Multivariate analysis indicated that males generally exhibited larger HRs and had higher movement rates and activity levels than females at all three sites. Contrary to our predictions, however, HR size and movement parameters did not vary across the sites in relation to the level of urbanization. At the urban site, individuals often crossed narrow roads and regularly used artificial structures as refuges for extended periods. Furthermore, the population sex ratio at the urban site was female-biased, consistent with the expectation that occupation of larger HRs and higher movement rates results in higher mortality for males in urbanized areas. Gila monsters did not appear to alter certain aspects of their spatial ecology in response to low levels of human activity but additional work will be required to assess population viability and possible effects in the long term and with higher levels of urbanization.
Geneland is a computer package that allows to make use of georeferenced individual multilocus genotypes for the inference of the number of populations and of the spatial location of genetic discontinuities between those populations. Main assumptions of the method are: (i) the number of populations is unknown and all values are considered a priori equally likely, (ii) populations are spread over areas given by a union of some polygons of unknown location in the spatial domain, (iii) Hardy–Weinberg equilibrium is assumed within each population and (iv) allele frequencies in each population are unknown and treated as random variable either following the so-called Dirichlet model or Falush model. Different algorithms implemented in Geneland to perform inferences are first briefly presented. Then major running steps and outputs (i.e. histogram of number of populations and map of posterior probabilities of population membership) are illustrated from the analysis of a simulated data set, which was also produced by Geneland.
There has been a recent trend in genetic studies of wild populations where researchers have changed their sampling schemes
from sampling pre-defined populations to sampling individuals uniformly across landscapes. This reflects the fact that many
species under study are continuously distributed rather than clumped into obvious “populations”. Once individual samples are
collected, many landscape genetic studies use clustering algorithms and multilocus genetic data to group samples into subpopulations.
After clusters are derived, landscape features that may be acting as barriers are examined and described. In theory, if populations
were evenly sampled, this course of action should reliably identify population structure. However, genetic gradients and irregularly
collected samples may impact the composition and location of clusters. We built genetic models where individual genotypes
were either randomly distributed across a landscape or contained gradients created by neighbor mating for multiple generations.
We investigated the influence of six different sampling protocols on population clustering using program STRUCTURE, the most
commonly used model-based clustering method for multilocus genotype data. For models where individuals (and their alleles)
were randomly distributed across a landscape, STRUCTURE correctly predicted that only one population was being sampled. However,
when gradients created by neighbor mating existed, STRUCTURE detected multiple, but different numbers of clusters, depending
on sampling protocols. We recommend testing for fine scale autocorrelation patterns prior to sample clustering, as the scale
of the autocorrelation appears to influence the results. Further, we recommend that researchers pay attention to the impacts
that sampling may have on subsequent population and landscape genetic results.
In the Sonoran Desert of North America, populations of the desert tortoise (Gopherus agassizii) occur in rocky foothills throughout southwestern Arizona and northwestern Mexico. Although tortoise populations appear to be isolated from each other by low desert valleys, individuals occasionally move long distances between populations. Increasingly, these movements are hindered by habitat fragmentation due to anthropogenic landscape changes. We used molecular techniques and radiotelemetry to examine movement patterns of desert tortoises in southern Arizona. We collected blood samples from 170 individuals in nine mountain ranges and analyzed variability in seven microsatellite loci to determine genetic differentiation among populations. Gene flow estimates between populations indicate that populations exchanged individuals historically at a rate greater than one migrant per generation, and positive correlation between genetic and geographic distance of population pairs suggests that the limiting factor for gene flow among populations is isolation by distance. Life history traits of the desert tortoise, a long-lived species with delayed sexual maturity, may severely constrain the ability of small populations to respond to disturbances that increase adult mortality. Historic gene flow estimates among populations suggests that recovery of declining populations may rely heavily on the immigration of new individuals from adjacent mountain ranges. Management strategies compatible with the evolutionary history of gene flow among disjunct populations will help ensure the long-term persistence of Sonoran desert tortoise populations.
Four variable microsatellite loci were used toexamine the genetic diversity and differentiation of golden lion tamarins (Leontopithecus rosalia) in four populations recently isolated by habitat fragmentation. Using Rst estimates of genetic differentiation, a considerable genetic divergence was detected among these populations, with an averagedifferentiation of 31%. Significant differences in allele number among these populations were found. However, the heterozygosity among these populations was not statistically different. These results suggestthat loss in allele diversity was faster than loss in heterozygosity. Conservation implications, particularly for golden lion tamarins, are then discussed. Loss of allelic diversity might be as serious a concern to endangered species as heterozygosity or inbreeding.
We present STRUCTURE HARVESTER (available at http://taylor0.biology.ucla.edu/structureHarvester/), a web-based program for collating results generated by the program STRUCTURE. The program provides a fast way to assess
and visualize likelihood values across multiple values of K and hundreds of iterations for easier detection of the number of genetic groups that best fit the data. In addition, STRUCTURE
HARVESTER will reformat data for use in downstream programs, such as CLUMPP.
KeywordsStructure–Population structure–Population genetics–Evanno method–Visualization–Clustering
The Gila Monster (Heloderma suspectum) is a large, venomous lizard protected throughout its distribution in the southwestern United States and northwestern Mexico. Rapid urban growth in key areas of its range and increased encounters with humans prompted us to investigate translocation as a conservation tool with “nuisance” Gila Monsters. Twenty-five Gila Monsters reported as nuisances by residents in the northeastern Phoenix Metropolitan Area were translocated from 0 to 25,000 m from their point of capture. Subjects (N=18) translocated less than 1000 m returned to their original site of capture within 2–30 days; none of those (N=7) translocated more than 1000 m successfully returned, they exhibited high daily rates of speed, and were deprived the use of familiar refuges. We conclude that small distance translocations within suitable habitats are ineffective in removing Gila Monsters from areas deemed unsuitable. Moreover, individuals moved significantly greater distances are unlikely to remain at a translocation site, and may experience a variety of costs (e.g., predation risk) associated with high rates of movement.
We introduce a method for analyzing phylogenies of genes sampled from a geographically structured population. A parsimony method can be used to compute s, the minimum number of migration events between pairs of populations sampled, and the value of s can be used to estimate the effective migration rate M, the value of Nm in an island model with local populations of size N and a migration rate m that would yield the same value of s. Extensive simulations show that there is a simple relationship between M and the geographic distance between pairs of samples in one- and two-dimensional models of isolation by distance. Both stepping-stone and lattice models were simulated. If two demes k steps apart are sampled, then, s, the average value of s, is a function only of k/(Nm) in a one-dimensional model and is a function only of k/(Nm)2 in a two-dimensional model. Furthermore, log(M) is approximately a linear function of log(k). In a one-dimensional model, the regression coefficient is approximately -1 and in a two-dimensional model the regression coefficient is approximately -0.5. Using data from several locations, the regression of log(M) on log(distance) may indicate whether there is isolation by distance in a population at equilibrium and may allow an estimate of the effective migration rate between adjacent sampling locations. Alternative methods for analyzing DNA sequence data from a geographically structured population are discussed. An application of our method to the data of R. L. Cann, M. Stoneking and A. C. Wilson on human mitochondrial DNA is presented.
When a population experiences a reduction of its effective size, it generally develops a heterozygosity excess at selectively neutral loci, i.e., the heterozygosity computed from a sample of genes is larger than the heterozygosity expected from the number of alleles found in the sample if the population were at mutation drift equilibrium. The heterozygosity excess persists only a certain number of generations until a new equilibrium is established. Two statistical tests for detecting a heterozygosity excess are described. They require measurements of the number of alleles and heterozygosity at each of several loci from a population sample. The first test determines if the proportion of loci with heterozygosity excess is significantly larger than expected at equilibrium. The second test establishes if the average of standardized differences between observed and expected heterozygosities is significantly different from zero. Type I and II errors have been evaluated by computer simulations, varying sample size, number of loci, bottleneck size, time elapsed since the beginning of the bottleneck and level of variability of loci. These analyses show that the most useful markers for bottleneck detection are those evolving under the infinite allele model (IAM) and they provide guidelines for selecting sample sizes of individuals and loci. The usefulness of these tests for conservation biology is discussed.
We describe a model-based clustering method for using multilocus genotype data to infer population structure and assign individuals to populations. We assume a model in which there are K populations (where K may be unknown), each of which is characterized by a set of allele frequencies at each locus. Individuals in the sample are assigned (probabilistically) to populations, or jointly to two or more populations if their genotypes indicate that they are admixed. Our model does not assume a particular mutation process, and it can be applied to most of the commonly used genetic markers, provided that they are not closely linked. Applications of our method include demonstrating the presence of population structure, assigning individuals to populations, studying hybrid zones, and identifying migrants and admixed individuals. We show that the method can produce highly accurate assignments using modest numbers of loci—e.g., seven microsatellite loci in an example using genotype data from an endangered bird species. The software used for this article is available from http://www.stats.ox.ac.uk/~pritch/home.html.
In most species the offspring of closely related parents have reduced fitness compared with the offspring of unrelated parents, a phenomenon known as inbreeding depression. However if parents are very distantly related, their offspring may also have reduced fitness. This pattern, outbreeding depression, has been most commonly observed in plants and only rarely in animals. Here we examine the consequences of inbreeding and outbreeding on juvenile survival of reintroduced Arabian oryx (Oryx leucoryx) in Oman, a population with a small number of founders drawn from a number of sources. Using microsatellite-based measures of inbreeding and outbreeding, there was no apparent relationship between inbreeding or outbreeding and survival when inbreeding and outbreeding were tested in separate statistical models. However when inbreeding and outbreeding were tested in the same statistical model, we found simultaneous inbreeding depression and outbreeding depression acting on juvenile survival. Outbreeding depression may be more common in vertebrates than previously supposed, and conservation strategies that seek to maximize the genetic diversity of managed populations may risk mixing lineages that are sufficiently differentiated to cause outbreeding depression among descendants.
Identification of individuals in a free-ranging animal population is potentially hampered by a lack of distinguishing features (e.g., scars, unique color patterns), poor visibility (e.g., densely forested environments), cost and invasiveness of physical capture, and mark loss. Advances in DNA-analysis technology offer alternative methods of individual identification that may overcome several of these problems. We investigated the genetic variability of American black bears (Ursus americanus) and brown (grizzly) bears (Ursus arctos) in the Columbia River basin of British Columbia, Canada, and developed a method to obtain genetic samples from free-ranging bears. We established the background genetic variability using microsatellite genotyping at 9 loci using tissue and blood samples from captured bears. In 3 field trials, we tested methods to obtain hair from free-ranging bears. Although all methods collected hair suitable for DNA analysis, the barbed-wire enclosure hair-trap was superior. We extracted DNA from hair roots and identified sample species with a species-specific mitochondrial DNA (mtDNA) test and sample sex from a Y-chromosome test. Using 6 microsatellite loci from nuclear DNA (nDNA), we screened all hair samples for individual identity and developed match probability functions based on scenarios of random sampling (P(random)), the likely presence of parent-offspring groupings in the samples (P(par-offs)), and the likely presence of siblings in the samples (P(sib)). We applied the P(sib) to each hair sample (match criteria at P(sib)<0.05) and illustrated how these microsatellite genotypes can be used as genetic tags in mark recapture bear censuses. The ability to identify species, sex, and individuality of free-ranging bears has numerous potential applications in field studies.
Effective population size is a fundamental parameter in population genetics, evolutionary biology and conservation biology, yet its estimation can be fraught with difficulties. Several methods to estimate Ne from genetic data have been developed which take advantage of various approaches for inferring Ne . The ability of these methods to accurately estimate Ne , however, has not been comprehensively examined. In this study, we employ seven of the most cited methods for estimating Ne from genetic data (Colony2, CoNe, Estim, MLNe, ONeSAMP, TMVP, and NeEstimator including LDNe) across simulated datasets with populations experiencing migration or no migration. The simulated population demographies are an isolated population with no immigration, an island model metapopulation with a sink population receiving immigrants, and an isolation by distance stepping stone model of populations. We find considerable variance in performance of these methods, both within and across demographic scenarios, with some methods performing very poorly. The most accurate estimates of Ne can be obtained by using LDNe, MLNe, or TMVP; however each of these approaches is outperformed by another in a differing demographic scenario. Knowledge of the approximate demography of population as well as the availability of temporal data largely improves Ne estimates. This article is protected by copyright. All rights reserved.
This article is protected by copyright. All rights reserved.
Bog Turtles (Glyptemys muhlenbergii) are imperiled by habitat loss and degradation; yet, population responses to habitat management and restoration efforts have not been well documented because of the difficulties of studying this long-lived species. We compared Bog Turtle population demography and habitat use from 1994 to 2009 at two sites in Massachusetts, USA: one site was managed for nonnative invasive species and natural succession (Site 1), and the other site was flooded from American Beaver (Castor canadensis) activity resulting in an expansion of nonnative invasive plants (Site 2). A mark–recapture study involving 90 individual turtles indicated that survival rates and population sizes remained stable before and after habitat management at Site 1 where the extent of high suitable habitat remained the same, whereas population size and survival rates declined at Site 2 where the extent of low suitable habitat increased. Together, these results suggest that habitat management and restoration efforts can improve or maintain the status of Bog Turtle populations. This study supports the value of properly planned and enacted habitat management actions for this federally threatened and state endangered species.
Since the data resulting from modern genotyping tools are astoundingly complex, genotyping studies require great care in the sampling design, genotyping, data analysis and interpretation. Such care is necessary because, with datasets containing thousands of loci, small biases can easily become strongly significant patterns. Such biases may already be present in routine tasks that are present in almost every genotyping study. Here, I discuss seven common mistakes that can be frequently encountered in the genotyping literature: (i) giving more attention to genotyping than to sampling; (ii) failing to perform or report experimental randomisation in the lab; (iii) equating geopolitical borders with biological borders; (iv) testing significance of clustering output; (v) misinterpreting Mantel's r statistic; (vi) only interpreting a single value of k; (vii) forgetting that only a small portion of the genome will be associated with climate. For every of those issues, I give some suggestions how to avoid these mistakes. Overall, I argue that genotyping studies would benefit from establishing a more rigorous experimental design, involving proper sampling design, randomisation and better distinction of a priori hypotheses and exploratory analyses. This article is protected by copyright. All rights reserved.
This article is protected by copyright. All rights reserved.
The endangered Mauna Kea silversword (Argyroxiphium sandwicense ssp. sandwicense) has experienced a severe decline in distribution and abundance because of predation by alien ungulates. By the late 1970s only a small remnant natural population persisted on the Mauna Kea volcano on the Island of Hawaii. The Hawaii Department of Land and Natural Resources, Division of Forestry and Wildlife, initiated an outplanting program in the 1970s to promote recovery of A. sandwicense ssp. sandwicense. Intermittent outplanting since 1973 has generated an outplanted population of over 450 plants on Mauna Kea, but the program has unintentionally resulted in a major population bottleneck. All plants in the outplanted population appear to be first- or subsequent-generation offspring of only two maternal founders from the natural population. Genetic variation in the natural and outplanted populations was assessed for 90 random amplified polymorphic DNA loci. Eleven loci were detectably polymorphic in the natural population, whereas only three loci were detectably polymorphic in the outplanted population. Thus, the population bottleneck has been accompanied by a 73% reduction in the level of detectable polymorphism. In addition, for eight loci, the population bottleneck has resulted in the loss of the marker allele in the outplanted population. A management strategy involving manual pollen transfer has recently been implemented to incorporate additional founders from the natural population into the outplanting program. As a supplement to the outplanting program, the strategy also includes a program promoting direct seedling establishment following manual pollen transfer. Incorporating additional founders may serve to overcome the legacy of the population bottleneck, especially if founder representation can be equalized.
We used Illumina paired-end shotgun sequencing to characterize microsatellite loci in Heloderma suspectum. We identified over 124,000 potentially amplifiable loci and describe PCR primers for 18 variable tri- and tetra-nucleotide STRs. The observed number of alleles per locus ranged from 5 to 16 and heterozygosity varied from 0.64 to 0.92. In addition 13 of these loci cross-amplified in the beaded lizard, Heloderma horridum. This method of microsatellite identification proved extremely efficient and cost effective. This novel marker set can be used by researchers to better understand these elusive species.
Abstract Six polymorphic microsatellite loci were isolated and characterized in the threatened Mexican beaded lizard, Heloderma horridum. The number of alleles per locus ranged from three to 12, with observed heterozygosity estimates ranging from 0.00 to 0.77, and expected heterozygosity estimates ranging from 0.00 to 0.73. These microsatellites will provide a valuable tool for the investigation of the genetic variation and structure of both wild and captive H. horridum populations.
In most species the offspring of closely related parents have reduced fitness compared with the offspring of unrelated parents, a phenomenon known as inbreeding depression. However if parents are very distantly related, their offspring may also have reduced fitness. This pattern, outbreeding depression, has been most commonly observed in plants and only rarely in animals. Here we examine the consequences of inbreeding and outbreeding on juvenile survival of reintroduced Arabian oryx (Oryx
leucoryx) in Oman, a population with a small number of founders drawn from a number of sources. Using microsatellite-based measures of inbreeding and outbreeding, there was no apparent relationship between inbreeding or outbreeding and survival when inbreeding and outbreeding were tested in separate statistical models. However when inbreeding and outbreeding were tested in the same statistical model, we found simultaneous inbreeding depression and outbreeding depression acting on juvenile survival. Outbreeding depression may be more common in vertebrates than previously supposed, and conservation strategies that seek to maximize the genetic diversity of managed populations may risk mixing lineages that are sufficiently differentiated to cause outbreeding depression among descendants.
Amphibians are often thought to have a metapopulation structure, which may render them vulnerable to habitat fragmentation. The red-spotted toad (Bufo punctatus) in the southwestern United States and Mexico commonly inhabits wetlands that have become much smaller and fewer since the late Pleistocene. This study tests two predictions based on metapopulation theory, that the incidence of habitat patch occupancy is directly related to patch size and that it is inversely related to patch isolation, and a third, potentially competing hypothesis, that patch occupancy is influenced by local environmental conditions. In a 20 000 km 2 area of the eastern Mojave Desert, 128 potential habitat patches (primarily springs) were identified and surveyed for local environmental characteristics and presence/ absence of B. punctatus. Patch size metrics reflected extent of water and riparian vegetation of several types. Patch isolation metrics were based on nearest-neighbor distances, cal-culated both as Euclidian distance and distance via connecting drainage channels. B. punc-tatus was found at 73% of the sites, including all of the 16 historic (pre-1970) sites. Patches were generally quite small, with water extending a median distance of only 200 m and median area of 72 m 2 . Median nearest-neighbor distances among patches were 1.8 km Euclidian distance (range: 0.4–22.0 km) and 6.8 km via drainage channels (range: 0.5– 64.9 km). Based on stepwise multiple logistic regression, the incidence of patch occupancy increased significantly with patch size and was also significantly related to elevation, lat-itude, and four metrics that were associated with rocky terrain, periodic scouring water flows, and ephemeral water. In contrast, incidence of patch occupancy was not significantly related to patch isolation. These findings are consistent with a ''patchy population'' model, rather than the classical equilibrium metapopulation model, implying frequent dispersal among patches and virtually no local extinctions. We speculate that B. punctatus in the Mojave Desert today occurs primarily in a patchy population or populations within mountain ranges that are isolated from patchy populations in other ranges. The influence of local environmental characteristics on patch occupancy demonstrates the importance of including patch quality metrics in tests of predictions for patch occupancy based on metapopulation theory.
The Mexican wolf (Canis lupus baileyi), an endangered subspecies of gray wolf, was native to parts of Mexico and the southwestern United States. Currently, only a few individuals, if any, exist in the wild, so planned reintroduction programs must use captive-raised wolves. In only one captive population, however, designated the certified lineage, are all the founders (n = 4) known to be obtained from a wild population of Mexican wolves. Two captive populations were founded from individuals of uncertain ancestry and have not been included in the species survival plan. To preserve genetic diversity and reduce inbreeding so that fitness will be maintained, it would be desirable to include these two captive populations in the breeding program if it could be shown that they were derived from a wild population similar to the certified lineage. We compared allele frequencies of 10 hypervariable microsatellite loci in Mexican gray wolves with those found in a sample of 42 domestic dogs, 151 northern gray wolves, and 142 coyotes to determine if uncertified Mexican wolves had specific markers from these animals. We analyzed pairwise genetic distance measures to demonstrate that the three captive populations of Mexican gray wolves were closely related to each other and distinct from dogs and northern gray wolves. The three captive populations are genetically more similar to each other than to any other population of dog or wolf-like canid, and they shared alleles that were rare in other canids. The genetic distance between them is similar to that between closely spaced populations of northern gray wolves. As a group, moreover, they are the most genetically distinct population of North American gray wolf. Therefore, the three captive populations could potentially be interbred to augment the genetic diversity of the certified lineage. Source individuals for reintroduction should be derived from the captive Mexican wolf population rather than populations of captive or wild northern gray wolves.
El lobo Mexicano (Canis lupus baileyi) nativo de algunas partes de México y el suroeste de los Estados Unidos, es una subespecie del lobo gris que se encuentra en peligro de extinción. En la actualidad solo unos cuantos organismos (y posiblemente ninguno) viven en estado salvaje, de tal forma que los programas de reintroducción tienen que hacerse con lobos mantenidos en cautiverio. Sin embargo, en una sola población cautiva de linaje certificado se encuentran todos los organismos fundadores (n = 4) conocidos por haber sido obtenidos de una población silvestre de lobos mexicanos. Dos poblaciones cautivas fueron fundadas con individuos de incierta procedencia y no han sido incluidas en el plan de supervivencia de especies. Para preservar la diversidad genética y reducir la consanguinidad de tal forma que la buena condición de la población se mantenga, sería deseable incluir estas dos poblaciones cautivas en el programa de reproducción siempre y cuando se demuestre que los organismos provienen de una población silvestre similar a la línea certificada. Con la finalidad de determinar si los lobos mexicanos sin certificar presentaban marcadores específicos comparamos las frecuencias alélicas de 10 loci microsatélites hipervariables en lobos grises mexicanos con aquellos obtenidos de una muestra de 42 perros domésticos, 151 lobos grises del norte y 142 coyotes. Se empleó el análisis de comparaciones pareadas de las medidas cde distancia genética, para demostrar que las tres poblaciones cautivas de lobos mexicanos se encuentran estrechamente relacionadas entre sí y distanciadas de cualquier otra población de perros o cánidos relacionados con lobos, así como para demostrar que comparten alelos raros en otros cánidos. La distancia genética entre ellos es similar a las encontradas para poblaciones cercanas de lobo gris del norte. Como grupo, estos animales además conforman la población de lobos grises genéticamente más distintiva de norteamérica. Por lo tanto, las tres poblaciones cautivas pueden ser potencialmente apareadas entre sí para aumentar la diversidad genética del linaje certificado. Los individuos empleados para la reintroducción deberán provenir de las poblaciones cautivas de lobos mexicanos, en lugar de aquellas cautivas o silvetres de lobos grises del norte.
In analysis of multilocus genotypes from structured populations, individual coefficients of membership in subpopulations are often estimated using programs such as structure. distruct provides a general method for visualizing these estimated membership coefficients. Subpopulations are represented as colours, and individuals are depicted as bars partitioned into coloured segments that correspond to membership coefficients in the subgroups. distruct, available at http://www.cmb.usc.edu/~noahr/distruct.html, can also be used to display subpopulation assignment probabilities when individuals are assumed to have ancestry in only one group.
We examined genetic variation, population structure, and definition of conservation units in Spotted Owls (Strix occidentalis). Spotted Owls are mostly non-migratory, long-lived, socially monogamous birds that have decreased population viability due to their occupation of highly-fragmented late successional forests in western North America. To investigate potential effects of habitat fragmentation on population structure, we used random amplified polymorphic DNA (RAPD) to examine genetic variation hierarchically among local breeding areas, subregional groups, regional groups, and subspecies via sampling of 21 breeding areas (276 individuals) among the three subspecies of Spotted Owls. Data from 11 variable bands suggest a significant relationship between geographic distance among local breeding groups and genetic distance (Mantel r = 0.53, P < 0.02) although multi-dimensional scaling of three significant axes did not identify significant grouping at any hierarchical level. Similarly, neighbor-joining clustering of Manhattan distances indicated geographic structure at all levels and identified Mexican Spotted Owls as a distinct clade. RAPD analyses did not clearly differentiate Northern Spotted Owls from California Spotted Owls. Among Northern Spotted Owls, estimates of population differentiation (F-ST) ranged from 0.27 among breeding areas to 0.11 among regions. Concordantly, within-group agreement values estimated via multi-response permutation procedures of Jaccard's distances ranged from 0.22 among local sites to 0.11 among regions. Pairwise comparisons of F-ST and geographic distance within regions suggested only the Klamath region was in equilibrium with respect to gene flow and genetic drift. Merging nuclear data with recent mitochondrial data provides support for designation of an Evolutionary Significant Unit for Mexican Spotted Owls and two overlapping Management Units for Northern and California Spotted Owls.
Bighorn sheep populations experienced a drastic reduction in both distribution and abundance until the advent of modern wildlife management, where improving viability of extant populations and translocating animals into historical habitat range have been the most important management policies. The fact that subspecies relationships among bighorn are ambiguous,together with the importance of selecting appropriate source stock and the expense of translocation projects, makes an understanding of subspecies relationships and genetic variation, within and between populations, important for the management and conservation of this species. In this study, genetic variation in 279 bighorn sheep from 13 study sites in Arizona, California, New Mexico and Alberta, Canada were examined by analyzing ten microsatellite loci to determine interpopulation differentiation and relationships between closely related taxa. All populations contained a substantial amount of genetic variation. Genetic differences between populations were large and roughly proportional to geographic distance. The significance of this to desert subspecies relationships and management is discussed.
DNA degradation, low DNA concentrations and primer-site mutations may result in the incorrect assignment of microsatellite genotypes, potentially biasing population genetic analyses. MICRO-CHECKER is WINDOWS(R)-based software that tests the genotyping of microsatellites from diploid populations. The program aids identification of genotyping errors due to nonamplified alleles (null alleles), short allele dominance (large allele dropout) and the scoring of stutter peaks, and also detects typographic errors. MICRO-CHECKER estimates the frequency of null alleles and, importantly, can adjust the allele and genotype frequencies of the amplified alleles, permitting their use in further population genetic analysis.
I describe a method of analysis of genetic differentiation which is suitable for the comparison of genetic and demographic estimates of the ‘neighborhood size’ – more precisely the product of density and second moment of dispersal distance σ2 – in continuous populations sampled at the smallest scale. This method is based on results of models of isolation by distance common to a wide variety of dispersal distances. The performance of this method is tested by simulation for some highly leptokurtic dispersal distributions, and it is applied to a previous study of a kangaroo-rat (Dipodomys spectabilis) population. In this case, genetic and demographic estimates are within a factor of two from each other. Thus, in line with some previous examples, this study shows that a better agreement may be attained than is usually recognized between genetic and demographic estimates.